Planta

, Volume 230, Issue 4, pp 659–669 | Cite as

Conserved microRNAs and their targets in model grass species Brachypodium distachyon

Original Article

Abstract

MicroRNAs are small, non-protein-coding RNAs playing regulatory functions in many organisms. Using computational approaches 26 new Brachypodium distachyon miRNAs belonging to 19 miRNA families were identified in expressed sequence tags (EST) and genomic survey sequence databases. EST revealed that predicted miRNAs are expressed in B. distachyon. Detailed nucleotide analyses showed that pre-miRNAs in B. distachyon are in the range of 63–180 nucleotides. Mature miRNAs located in the different positions of precursor RNAs are varied from 19 to 24 nucleotides in length. Quantifying RNAs using realtime PCR (qRT-PCR) analyses validated expression level differences of selected B. distachyon miRNAs. In this study, we detected that the expression level of some of the predicted miRNAs are distinct and some of them are similar in the leaf tissues. In addition, using these miRNAs as queries 27 potential target mRNAs were predicted in B. distachyon NCBI EST database and 246 target mRNA were predicted in NCBI protein-coding nucleotide (mRNA) database of all plant species. The majority of the target mRNAs encode transcription factors regulating plant development, morphology and flowering time. Other newly identified miRNAs target the mRNAs involving metabolic processes, signal transduction and stress response.

Keywords

Brachypodium distachyon MicroRNA Stem–loop hairpin structure Expressed sequence tag Genomic survey sequence Target mRNA qRT-PCR 

Abbreviations

ΔG

Folding-free energies

AGO1

Argonaute-1

Ap2

APETALA2

ARF

Auxin response transcription factor

DCL1

Dicer-like protein

GSS

Genomic survey sequence

miRNA

MicroRNA

RT

Real time

EST

Expressed sequence tag

DCL1

Dicer-like protein

EREBPs

Ethylene-responsive element-binding proteins

MFE

Minimal folding-free energy

MFEI

Minimal folding-free energy index

miRNA*

Opposite miRNA sequence

NCBI

National Center of Biotechnology Information

Nt

Nucleotide(s)

pre-miRNA

MicroRNA precursor

pri-miRNAs

MicroRNA primary

RISC

RNA-induced silencing complex

qRT-PCR

Quantitative real-time PCR

SBP

Squamosa promoter-binding proteins

Ser

Serine

SPL

SBP-like proteins

Thr

Threonine

Notes

Acknowledgment

We would like to thank Mine Bakar for technical assistance in performing qRT-PCR experiments.

Supplementary material

425_2009_974_MOESM1_ESM.doc (44 kb)
Supplementary material 1 (DOC 44 kb)
425_2009_974_MOESM2_ESM.doc (50 kb)
Supplementary material 2 (DOC 49 kb)
425_2009_974_MOESM3_ESM.doc (182 kb)
Supplementary material 3 (DOC 182 kb)

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Copyright information

© Springer-Verlag 2009

Authors and Affiliations

  1. 1.Biological Sciences and Bioengineering Program, Faculty of Engineering and Natural SciencesSabanci UniversityIstanbulTurkey
  2. 2.Kocaeli UniversityIzmitTurkey

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